Turmoil at the National Security Council, From the Top Down

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Michael T. Flynn, left, the national security adviser, before boarding Air Force One on Friday. He accompanied President Trump and Japan’s prime minister, Shinzo Abe, on a visit to Mar-a-Lago, Mr. Trump’s club in Palm Beach, Fla.CreditCreditAl Drago/The New York Times

Over the weekend, The Times published this investigation into the agency that Michael T. Flynn was leading before he stepped down. Read our updated article on Mr. Flynn’s resignation.

WASHINGTON — These are chaotic and anxious days inside the National Security Council, the traditional center of management for a president’s dealings with an uncertain world.

Three weeks into the Trump administration, council staff members get up in the morning, read President Trump’s Twitter posts and struggle to make policy to fit them. Most are kept in the dark about what Mr. Trump tells foreign leaders in his phone calls. Some staff members have turned to encrypted communications to talk with their colleagues, after hearing that Mr. Trump’s top advisers are considering an “insider threat” program that could result in monitoring cellphones and emails for leaks.

The national security adviser, Michael T. Flynn, has hunkered down since investigators began looking into what, exactly, he told the Russian ambassador to the United States about the lifting of sanctions imposed in the last days of the Obama administration, and whether he misled Vice President Mike Pence about those conversations. His survival in the job may hang in the balance.

Although Mr. Trump suggested to reporters aboard Air Force One on Friday that he was unaware of the latest questions swirling around Mr. Flynn’s dealings with Russia, aides said over the weekend in Florida — where Mr. Flynn accompanied the president and Japan’s prime minister, Shinzo Abe — that Mr. Trump was closely monitoring the reaction to Mr. Flynn’s conversations. There are transcripts of a conversation in at least one phone call, recorded by American intelligence agencies that wiretap foreign diplomats, which may determine Mr. Flynn’s future.

Stephen Miller, the White House senior policy adviser, was circumspect on Sunday about Mr. Flynn’s future. Mr. Miller said on NBC’s “Meet the Press” that possibly misleading the vice president on communications with Russia was “a sensitive matter.” Asked if Mr. Trump still had confidence in Mr. Flynn, Mr. Miller responded, “That’s a question for the president.”

This account of life inside the council — offices made up of several hundred career civil servants who advise the president on counterterrorism, foreign policy, nuclear deterrence and other issues of war and peace — is based on conversations with more than two dozen current and former council staff members and others throughout the government. All spoke on the condition that they not be quoted by name for fear of reprisals.

“It’s so far a very dysfunctional N.S.C.,” Representative Adam B. Schiff of California, the senior Democrat on the House Intelligence Committee, said in a telephone interview.

In a telephone conversation on Sunday afternoon, K. T. McFarland, the deputy national security adviser, said that early meetings of the council were brisker, tighter and more decisive than in the past, but she acknowledged that career officials were on edge. “Not only is this a new administration, but it is a different party, and Donald Trump was elected by people who wanted the status quo thrown out,” said Ms. McFarland, a veteran of the Reagan administration who most recently worked for Fox News. “I think it would be a mistake if we didn’t have consternation about the changes — most of the cabinet haven’t even been in government before.”

There is always a shakedown period for any new National Security Council, whose staff is drawn from the State Department, the Pentagon and other agencies and is largely housed opposite the White House in the Eisenhower Executive Office Building.

President Barack Obama replaced his first national security adviser, Gen. James Jones, a four-star former supreme allied commander in Europe, after concluding that the general was a bad fit for the administration. The first years of President George W. Bush’s council were defined by clashes among experienced bureaucratic infighters — Dick Cheney, Donald Rumsfeld and Colin Powell among them — and by decisions that often took place outside official channels.

But what is happening under the Trump White House is different, officials say, and not just because of Mr. Trump’s Twitter foreign policy. (Two officials said that at one recent meeting, there was talk of feeding suggested Twitter posts to the president so the council’s staff would have greater influence.)

A number of staff members who did not want to work for Mr. Trump have returned to their regular agencies, leaving a larger-than-usual hole in the experienced bureaucracy. Many of those who remain, who see themselves as apolitical civil servants, have been disturbed by displays of overt partisanship. At an all-hands meeting about two weeks into the new administration, Ms. McFarland told the group it needed to “make America great again,” numerous staff members who were there said.

New Trump appointees are carrying coffee mugs with that Trump campaign slogan into meetings with foreign counterparts, one staff member said.

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Michael T. Flynn served in the military for 33 years before becoming a singular and divisive figure in the intelligence community during the Obama administration. Matthew Rosenberg looks at President Trump’s former national security adviser.Published OnJan. 18, 2017CreditCreditKevin Hagen for The New York Times

Nervous staff members recently met late at night at a bar a few blocks from the White House and talked about purging their social media accounts of any suggestion of anti-Trump sentiments.

Mr. Trump’s council staff draws heavily from the military — often people who had ties to Mr. Flynn when he served as a senior military intelligence officer and then as the director of the Defense Intelligence Agency before he was forced out of the job. Many of the first ideas that have been floated have involved military, rather than diplomatic, initiatives.

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Mr. Trump and Defense Secretary Jim Mattis arriving at the Pentagon last month. Mr. Mattis did not see a number of executive orders before they were issued.CreditStephen Crowley/The New York Times

Last week, Defense Secretary Jim Mattis was exploring whether the Navy could intercept and board an Iranian ship to look for contraband weapons possibly headed to Houthi fighters in Yemen. The potential interdiction seemed in keeping with recent instructions from Mr. Trump, reinforced in meetings with Mr. Mattis and Secretary of State Rex W. Tillerson, to crack down on Iran’s support of terrorism.

But the ship was in international waters in the Arabian Sea, according to two officials. Mr. Mattis ultimately decided to set the operation aside, at least for now. White House officials said that was because news of the impending operation leaked, a threat to security that has helped fuel the move for the insider threat program. But others doubt whether there was enough basis in international law, and wondered what would happen if, in the early days of an administration that has already seen one botched military action in Yemen, American forces were suddenly in a firefight with the Iranian Navy.

Ms. McFarland often draws on her television experience to make clear to officials that they need to make their points in council meetings quickly, and she signals when to wrap up, several participants said.

And while Mr. Obama liked policy option papers that were three to six single-spaced pages, council staff members are now being told to keep papers to a single page, with lots of graphics and maps.

“The president likes maps,” one official said.

Paper flow, the lifeblood of the bureaucracy, has been erratic. A senior Pentagon official saw a draft executive order on prisoner treatment only through unofficial rumors and news media leaks. He called the White House to find out if it was real and said he had concerns but was not sure if he was authorized to make suggestions.

Officials said that the absence of an orderly flow of council documents, ultimately the responsibility of Mr. Flynn, explained why Mr. Mattis and Mike Pompeo, the director of the C.I.A., never saw a number of Mr. Trump’s executive orders before they were issued. One order had to be amended after it was made public, to reassure Mr. Pompeo that he had a regular seat on the council.

White House officials say that was a blunder, and that the process of reviewing executive orders has been straightened out by Reince Priebus, the White House chief of staff.

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Stephen K. Bannon, center, Mr. Trump’s top strategist, who was made a member of the National Security Council two weeks ago.CreditStephen Crowley/The New York Times

Still, Mr. Flynn presents additional complications beyond his conversations with the Russian ambassador. His aides say he is insecure about whether his unfettered access to Mr. Trump during the campaign is being scaled back and about a shadow council created by Stephen K. Bannon, Mr. Trump’s top strategist, who was invited to attend meetings of the “principals committee” of the council two weeks ago. For his part, Mr. Bannon sees the United States as headed toward an inevitable confrontation with two adversaries — China and Iran.

Mr. Flynn finds himself in a continuing conflict with the intelligence agencies, whose work on Russia and other issues he has dismissed as subpar and politically biased. Last week, in an incident first reported by Politico, one of Mr. Flynn’s top deputies, Robin Townley, was denied the high-level security clearance he needed before he could take up his job on the council as the senior director for Africa.

It was not clear what in Mr. Townley’s past disqualified him, and in every administration some officials are denied clearances. But some saw the intelligence community striking back.

Two people with direct access to the White House leadership said Mr. Flynn was surprised to learn that the State Department and Congress play a pivotal role in foreign arms sales and technology transfers. So it was a rude discovery that Mr. Trump could not simply order the Pentagon to send more weapons to Saudi Arabia — which is clamoring to have an Obama administration ban on the sale of cluster bombs and precision-guided weapons lifted — or to deliver bigger weapons packages to the United Arab Emirates.

Several staff members said that Mr. Flynn, who was a career Army officer, was not familiar with how to call up the National Guard in an emergency — for, say, a natural disaster like Hurricane Katrina or the detonation of a dirty bomb in an American city.

At the all-hands meeting, Mr. Flynn talked about the importance of a balanced work life, taking care of family, and using the time at the council to gain experience that would help staff members in other parts of the government. At one point, the crowd was asked for a show of hands of how many expected to be working at the White House in a year.

Mr. Flynn turned to Ms. McFarland and, in what seemed to be a self-deprecating joke, said, “I wonder if we’ll be here a year from now?”